SMTL ID : 5vn0.3 (3 other biounits)

Water-forming NADH oxidase from Lactobacillus brevis (LbNOX) bound to NADH.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 37 residues within 4Å: Chain A: G.57, C.58, T.59, H.60, A.61, Y.81, E.82, R.83, N.84, S.91, C.92, I.94, H.127, N.128, V.129, T.160, S.161, G.162, S.163, C.181, K.182, I.208, E.211, F.292, N.295, L.298, G.328, D.329, P.345, L.346, A.347, T.348, A.350 Chain B: F.472, Q.473 Ligands: OXY.2, NAI.3 33 PLIP interactions: 29 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.208 Hydrogen bonds: A:C.58, A:T.59, A:T.59, A:T.59, A:H.60, A:A.61, A:R.83, A:R.83, A:N.84, A:N.84, A:V.129, A:V.129, A:S.163, A:D.329, A:L.346, A:A.347, A:T.348, B:F.472 Water bridges: A:T.59, A:H.60, A:G.62, A:S.91, A:S.91, A:S.91, A:N.128, A:S.330, A:S.330, A:A.350, B:F.472, B:F.472, B:Q.473 Salt bridges: A:K.182 FAD.5: 36 residues within 4Å: Chain A: F.472, Q.473 Chain B: G.57, C.58, T.59, H.60, A.61, Y.81, E.82, R.83, N.84, S.91, C.92, I.94, H.127, N.128, V.129, T.160, S.161, G.162, S.163, C.181, K.182, I.208, F.292, N.295, L.298, G.328, D.329, P.345, L.346, A.347, T.348, A.350 Ligands: OXY.6, NAI.7 35 PLIP interactions: 31 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.208, B:I.208 Hydrogen bonds: B:C.58, B:T.59, B:T.59, B:H.60, B:A.61, B:R.83, B:R.83, B:N.84, B:V.129, B:V.129, B:S.163, B:D.329, B:L.346, B:A.347, B:T.348, A:F.472 Water bridges: B:T.59, B:T.59, B:T.59, B:N.84, B:S.91, B:S.91, B:S.91, B:N.128, B:N.295, B:S.330, B:S.330, B:A.350, B:A.350, A:F.472, A:F.472, A:Q.473 Salt bridges: B:K.182

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 5 residues within 4Å: Chain A: L.90, S.91, C.92 Chain B: F.472 Ligands: FAD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.91, A:C.92 OXY.6: 4 residues within 4Å: Chain A: F.472 Chain B: S.91, C.92 Ligands: FAD.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.91, B:C.92

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 27 residues within 4Å: Chain A: I.203, G.204, A.205, G.206, Y.207, I.208, E.211, I.226, D.227, A.228, M.229, P.234, K.235, Y.236, E.260, T.261, C.289, I.290, G.291, F.292, P.345, L.346, S.375, G.376, L.377 Chain B: Q.473 Ligands: FAD.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.207, A:I.208 Hydrogen bonds: A:Y.207, A:I.208, A:A.228, A:M.229, A:Y.236, A:Y.236, A:Y.236, A:G.291, A:P.345, A:G.376 Water bridges: A:G.206, A:G.209, A:F.292, A:G.376, A:G.376 Salt bridges: A:K.235 NAI.7: 25 residues within 4Å: Chain A: Q.473 Chain B: G.204, A.205, G.206, Y.207, I.208, E.211, I.226, D.227, A.228, M.229, P.234, K.235, Y.236, E.260, C.289, I.290, G.291, F.292, P.345, L.346, S.375, G.376, L.377 Ligands: FAD.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.207, B:I.208 Hydrogen bonds: B:Y.207, B:I.208, B:A.228, B:Y.236, B:Y.236, B:G.291, B:P.345, B:G.376 Water bridges: B:G.206, B:G.209, B:K.235, B:G.376, B:G.376 Salt bridges: B:K.235

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: F.64, Y.110 Chain B: R.478, P.479 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.478 EDO.8: 4 residues within 4Å: Chain A: R.478, P.479 Chain B: F.64, Y.110 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.478 EDO.9: 6 residues within 4Å: Chain A: V.366 Chain B: D.463, D.464, A.466, M.467, Q.491 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.491, B:Q.491 Water bridges: B:D.463, A:K.367, A:K.367 EDO.10: 8 residues within 4Å: Chain B: R.382, E.407, P.420, V.421, L.422, M.440, S.441, K.442 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.382, B:E.407, B:M.440 Water bridges: B:K.442

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cracan, V. et al., A genetically encoded tool for manipulation of NADP(+)/NADPH in living cells. Nat. Chem. Biol. (2017)

Release Date

2017-08-02

Peptides

NAD(FAD)-dependent dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

NAD(FAD)-dependent dehydrogenase

Related Entries With Identical Sequence